Sequence
atgc intronic sequence ATGC exonic sequencegtattctggttttgctttttcatttatatccctggtttggtttcttcaaatagactcactaggaagttgacaatgaaacttatttgcggtagctccttagtgccatttttggtttcctgtataatgtgtttcgccaaatatacaaaaccttttaaaaaaacatttacaattcctcagGTTGAGCTTAAGGAAGGCCCTCTGGAACAGTTCACACATGAGATGGAGCCCTTTCTACGCAAGCAAGGACTTCCAGTTCGCTTGAACAAAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G109133_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os11g01420.1 (Oryza sativa), 3'ss of exon 5
gtattctggttttgctttttcatttatatccctggtttggtttcttcaaatagactcactaggaagttgacaatgaa--acttatttgcggtagctccttagtgccatttttggtttcctgtataatgtgtttcgccaaatatacaaaaccttttaaaaaaacatttacaattcctcagGTTGAGCTTAAGGAAGGCCCTCTGGAACAGTTCACACATGAGATGGAGCCCTTTCTACGCAAGCAAGGACTTCCAGTTCGCTTGAACAAAG
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---------------------------------------------------------gctgtggtgtctgcaatgcacaatatgtctggaataactatt------cactttctcttcttcataaaacatggtttactaaatttagaaca----------------tgatgatatgtcagGTGGAGCTTAAGGAAGGCCCCTTGGAACAGTTTACACATGAAATGGAACCCTTTCTACGCAAGCAAGGACTGCCAGTTCGTCTGAACAAAG
upper sequence: GRMZM2G109133_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os12g01430.2 (Oryza sativa), 3'ss of exon 4
gtattctggttttgctttttcatttatatccctggtttggtttcttcaaatagactcactaggaagttgacaatgaaacttatttgcggtagctccttagtgccatttttggtttcctgtataatgtgtttcgccaaatatacaaaaccttttaaaaaaacatttacaattcctcagGTTGAGCTTAAGGAAGGCCCTCTGGAACAGTTCACACATGAGATGGAGCCCTTTCTACGCAAGCAAGGACTTCCAGTTCGCTTGAACAAAG
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-------------------------------------------------------tagctgtggtgtctgcaatgcacaatgtctggaataactatt------cactctctcttcttcataaaacatggtttactaaattta--gaacctg--------------atgatatgtcagGTGGAGCTTAAGGAAGGCCCCTTAGAACAGTTTACACATGAAATGGAACCCTTTCTACGCAAGCAAGGAATGCCAGTTCGTCTGAACAAAG
upper sequence: GRMZM2G109133_T01 (Zea mays), 3'ss of exon 3
lower sequence: AT1G25260.1 (Arabidopsis thaliana), 3'ss of exon 5
gtattctggttttgctttttcatttatatccctggtttggtttcttcaaatagactcactaggaagttgacaatgaaacttatttgcggtagctccttagtgccatttttggtttcctgtataatgtgtttcgccaaatatacaaaaccttttaaaaaaacatttac-aattcctcagGTTGAGCTTAAGGAAGGCCCTCTGGAACAGTTCACACATGAGATGGAGCCCTTTCTACGCAAGCAAGGACTTCCAGTTCGCTTGAACAAAG
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-----------------gtttgtgaacagaacttg--tgccatctctatatactgttgtttctagataaataaataagcttgactatgatcaggctctgcttc--tctttgttatttaaaaaactttgtttcgttacttttatcttaattactatattggtaccacctaaatgattagGTTGAACTGAAGGAAGGTCCTCTAGAACAGTTCACACATGAGATGGAACCACTTCTTCGGAAGCTTGAAATGCCTGTACGACTAAACAAAG
upper sequence: GRMZM2G109133_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv12s0034g01000.t01 (Vitis vinifera), 3'ss of exon 5
gtattctggttttgctttttcatttatatccctggtttggtttcttcaaatagactcactaggaagttgacaatgaaacttatttgcggtagctccttagtgccatttttggtttcctgtataatgtgtttcgccaaatata-caaaaccttttaaaa-aaacatttacaattcctcagGTTGAGCTTAAGGAAGGCCCTCTGGAACAGTTCACACATGAGATGGAGCCCTTTCTACGCAAGCAAGGACTTCCAGTTCGCTTGAACAAAG
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-------------------------------------------------------------------------------taaaacacagaaatctgtgatcatcttttcatattgcatatatgattcatctcatatatcctaacaaaatttcttgcattgaatccttaatatgtttcagGTGGAGCTTAAAGAAGGTCCTCTTGATCAGTTCACACATGAGATGGAACCCTTCCTACGCAAGCAAGGGATGCCGGTTCGGTTGAACAAAG
upper sequence: GRMZM2G109133_T01 (Zea mays), 3'ss of exon 3
lower sequence: EFJ38547 (Selaginella moellendorffii), 3'ss of exon 4
gtattctggttttgctttttcatttatatccctggtttggtttcttcaaatagactcactaggaagttgacaatgaaacttatttgcggtagctccttagtgccatttttggtttcctgtataatgtgtttcgccaaatatacaaaaccttttaaaaaaacatttacaattcctcagGTTGAGCTTAAGGAAGGCCCTCTGGAACAGTTCACACATGAGATGGAGCCCTTTCTACGCAAGCAAGGACTTCCAGTTCGCTTGAACAAAG
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----------------------------------------------------------------------------------------gt-gcgtgtagacaatgcttttgcttt--tgcgtggttttcttcgtgtagctcac-----------------tgtgagtgactacacagGTGGAACTCAACGAAGGCCCACTGGAGCAATTCACGCACGAGATGGAGCCATTTCTGCGAAAGCAAGGAATGCCTGTTCGTCTAAACAGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aatgtgtttcgccaaatatacaaaaccttttaaaaaaacatttacaattcctcagGTTGAGCTTAAGGAAGGCCCTCTGGAACAGTTCACACATGAGATGGAGCCCTTTCTACGCAAGCAAGGACTTCCAGTTCGCTTGAACAAAG
ttcctc CT-rich tract
aaatatacaaaacctt TA-rich tract
Putative cis-regulatory sequences
atgc | intron | ATGC | exonic elements by Pertea et al. |
ATGC | exon | atgc | putative intronic elements |
| | ATGC | putative exonic elements identified for retained introns |
10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtattctggttttgctttttcatttatatccctggtttggtttcttcaaatagactcactaggaagttgacaatgaaacttatttgcggtagctccttagtgccatttttggtttcctgtataatgtgtttcgccaaatatacaaaaccttttaaaaaaacatttacaattcctcagGTTGAGCTTAAGGAAGGCCCTCTGGAACAGTTCACACATGAGATGGAGCCCTTTCTACGCAAGCAAGGACTTCCAGTTCGCTTGAACAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG